Research workbench
Structural analysis of an exo-beta-agarase
Analyse Structural analysis of an exo-beta-agarase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BQ3
- Type
- protein
- Length
- 2,962 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- B-agarase
- EC
- 3.2.1.81
- UniProt
- Q21HC5
- Ligands
- 47N, CA
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 28% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | B-agarase (EC 3.2.1.81) | protein | 740 | 27% helix, 23% strand | Q21HC5 |
| B | B-agarase (EC 3.2.1.81) | protein | 741 | 28% helix, 23% strand | Q21HC5 |
| C | B-agarase (EC 3.2.1.81) | protein | 740 | 28% helix, 23% strand | Q21HC5 |
| D | B-agarase (EC 3.2.1.81) | protein | 741 | 27% helix, 24% strand | Q21HC5 |
Ligands and binding sites
- 47N · Neoagarobiose · ligand · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 27 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1113 | 0.79 | 0.80 | 111 | 47N, GOL |
| 2 | 1193 | 0.78 | 0.80 | 98 | 47N, GOL |
| 3 | 768 | 0.76 | 0.80 | 80 | 47N, GOL |
| 4 | 75 | 0.76 | 0.99 | 29 | GOL |
| 5 | 729 | 0.75 | 0.80 | 74 | 47N, GOL |
Interfaces
4 interfaces between chains.
- A–B · 926 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 292 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 253 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 74 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4BQ3 · Structural analysis of an exo-beta-agarase · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q21HC5
- Elsewhere: RCSB PDB 4BQ3 · PDBe 4BQ3 · UniProt Q21HC5
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